Complete Genome Sequences of Three Ornithobacterium rhinotracheale Strains from Avian Sources, Using Hybrid Nanopore-Illumina Assembly

Hashish, Amro; Johnson, Timothy J.; Smith, Emily; Chundru, Dhiraj; Williams, Michele L.; Macedo, Núbia; Sato, Yuko; Ghanem, Mostafa; El‐Gazzar, Mohamed

doi:10.1128/mra.01059-22

Cited by 1 publication

(4 citation statements)

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“…For high-resolution molecular characterization of ORT and PM, two recently developed cgMLST schemes [23,24] were utilized. The two cgMLST schemes were developed using Ridom SeqSphere + software version 8.3.1 (Munster, Germany, http://www.ridom.…”

Section: Molecular Characterizationmentioning

confidence: 99%

“…To date, ORT [ 15 ] and PM [ 16 , 17 ] remain a challenge in terms of timely identification, treatment and the prevention. In addition, PM has been more thoroughly investigated compared to ORT which is reflected by the seven complete avian ORT genomes available in GenBank ® ( , accessed on 7 July 2023) [ 18 ] compared to the 139 complete genomes for PM ( , accessed on 27 July 2023). The use of whole genome sequencing enables further isolate identification and serological characterization of genotypes including steps such as multi-loci sequence typing, virulence factor-encoding genes and whole genome phylogeny to establish evolutionary relationships and clonality among commercial turkey populations [ 2 , 19 , 20 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

“…In addition, PM has been more thoroughly investigated compared to ORT which is reflected by the seven complete avian ORT genomes available in GenBank ® (https://www.ncbi.nlm. nih.gov/genome/browse/#!/prokaryotes/10734/, accessed on 7 July 2023) [18] compared to the 139 complete genomes for PM (https://www.ncbi.nlm.nih.gov/genome/browse/#! /prokaryotes/912/, accessed on 27 July 2023).…”

Section: Introductionmentioning

confidence: 99%

“…Having a robust way to capture and analyze data upon the detection of emerging pathogens is of outmost importance to allow for a timely mitigation response for the prevention of disease spread. Recently, a TaqMan Real-Time Polymerase Chain Reaction (qPCR) has been developed for ORT [22] and a unique Core-Genome Multi-Locus Sequencing Typing cgMLST technique, tailored specifically for ORT [23] and PM [24] has recently been developed to aid in the characterization of these pathogens.…”

Section: Introductionmentioning

confidence: 99%

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Space–Time Patterns of Poultry Pathogens in the USA: A Case Study of Ornithobacterium rhinotracheale and Pasteurella multocida in Turkey Populations

Campler,

Hashish,

Ghanem

et al. 2023

Pathogens

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Respiratory infections caused by Ornithobacterium rhinotrachealis (ORT) and Pasteurella multocida (PM) bacteria are significant threats to the poultry industry by causing economic losses and welfare issues. Due to characterization difficulties and underutilization of epidemiological tools, description of the spatio-temporal spread of these diseases in the field is limited. The objectives of this retrospective observational cross-sectional study were to (a) investigate the existence of space–time clusters (hotspots); and (b) investigate the association between genetic similarity and spatial proximity for both pathogens using molecular typing and a recently developed Core-Genome Multilocus Sequencing Typing (cgMLST) scheme. ORT (n = 103) and PM (n = 69) isolates from confirmed disease outbreaks from one commercial company between 2013 and 2021 were obtained from a veterinary diagnostic laboratory, characterized using a cgMLST scheme and visualized using a minimum spanning tree. Spatio-temporal cluster analysis using SaTScanTM and a Spearman’s rank correlation were performed to investigate clustering and any association between allelic diversity and geospatial distance. The cgMLST sequencing revealed three allelic clusters for ORT and thirteen clusters for PM. The spatio-temporal analysis revealed two significant clusters for PM, one with a 259.3 km cluster containing six cases between May and July 2018 and a 9 km cluster containing five cases between February 2019 and February 2021. No spatio-temporal clusters were found for ORT. A weak negative correlation between allelic diversity and geospatial distance was observed for ORT (r = −0.04, p < 0.01) and a weak positive correlation was observed for PM (r = 0.11, p < 0.01). This study revealed regional spatio-temporal clusters for PM in commercial turkey sites between 2018 and 2021 and provided additional insight into bacterial strain subgroups and the geographical spread of ORT and PM over time.

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Section: Molecular Characterizationmentioning

confidence: 99%